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ORCIDBMC Systems Biology, Volume 1
Volume 1, 2007
- Ofer Meshi, Tomer Shlomi, Eytan Ruppin:
Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network. 1 - Steffen Klamt
, Julio Saez-Rodriguez, Ernst Dieter Gilles:
Structural and functional analysis of cellular networks with CellNetAnalyzer. 2 - Najaf A. Shah, Richard J. Laws, Bradley Wardman, Lue Ping Zhao, John L. Hartman IV:
Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays. 3 - Marc A. Schaub, Thomas A. Henzinger, Jasmin Fisher:
Qualitative networks: a symbolic approach to analyze biological signaling networks. 4 - Christoph Gille, Sabrina Hoffmann, Hermann-Georg Holzhütter:
METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks. 5 - Chunguang Li, Luonan Chen, Kazuyuki Aihara:
Stochastic synchronization of genetic oscillator networks. 6 - Vassilios Sotiropoulos, Yiannis N. Kaznessis:
Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes. 7 - Igor Ulitsky, Ron Shamir:
Identification of functional modules using network topology and high-throughput data. 8 - Sourabh Kharait, Sampsa Hautaniemi, Shan Wu, Akihiro Iwabu, Douglas A. Lauffenburger, Alan Wells:
Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. 9 - Rui Alves, Albert Sorribas:
In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. 10 - Florian Geier, Jens Timmer, Christian Fleck:
Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge. 11 - Laxman Yetukuri, Mikko Katajamaa, Gema Medina-Gómez, Tuulikki Seppänen-Laakso, Antonio Vidal-Puig, Matej Oresic:
Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis. 12 - William J. Bosl:
Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery. 13 - Jonathan Tang, Klaus Ley, C. Anthony Hunt:
Dynamics of in silico leukocyte rolling, activation, and adhesion. 14 - Pierre R. Bushel, Russell D. Wolfinger, Greg Gibson:
Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes. 15 - Luciano da F. Costa, Marcus Kaiser, Claus C. Hilgetag:
Predicting the connectivity of primate cortical networks from topological and spatial node properties. 16 - Carole J. Proctor, Maria Tsirigotis, Douglas A. Gray:
An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline. 17 - Tunahan Çakir, Betül Kirdar, Z. Ilsen Önsan, Kutlu Ö. Ülgen, Jens Nielsen:
Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae. 18 - Zheng Liu, S. Frank Yan, John R. Walker, Theresa A. Zwingman, Tao Jiang, Jing Li, Yingyao Zhou:
Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas. 19 - Chunnuan Chen, Matthew T. Weirauch, Corey Powell, Alexander C. Zambon, Joshua M. Stuart:
A search engine to identify pathway genes from expression data on multiple organisms. 20 - Zheng Li, Shireesh Srivastava, Xuerui Yang, Sheenu Mittal, Paul Norton, James H. Resau, Brian B. Haab, Christina Chan:
A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells. 21 - Tommi Aho, Olli-Pekka Smolander, Jari Niemi, Olli Yli-Harja:
RMBNToolbox: random models for biochemical networks. 22 - Andreas Hoppe, Sabrina Hoffmann, Hermann-Georg Holzhütter:
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. 23 - Jun Dong, Steve Horvath:
Understanding network concepts in modules. 24 - Helene M. Langevin, Donna M. Rizzo, James R. Fox, Gary J. Badger, Junru Wu, Elisa E. Konofagou, Debbie Stevens-Tuttle, Nicole A. Bouffard, Martin H. Krag:
Dynamic morphometric characterization of local connective tissue network structure in humans using ultrasound. 25 - Neema Jamshidi, Bernhard Ø. Palsson:
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. 26 - Sergii Ivakhno, J. Douglas Armstrong:
Non-linear dimensionality reduction of signaling networks. 27 - Nicolas Le Novère:
The long journey to a Systems Biology of neuronal function. 28 - Romain Bourqui, Ludovic Cottret, Vincent Lacroix, David Auber, Patrick Mary, Marie-France Sagot, Fabien Jourdan:
Metabolic network visualization eliminating node redundance and preserving metabolic pathways. 29 - Yohann Grondin, Derek J. Raine, Vic Norris:
The correlation between architecture and mRNA abundance in the genetic regulatory network of Escherichia coli. 30 - Hiroyuki Kurata, Quanyu Zhao, Ryuichi Okuda, Kazuyuki Shimizu:
Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. 31 - Arne B. Gjuvsland, Ben J. Hayes, Theo H. E. Meuwissen, Erik Plahte, Stig W. Omholt:
Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms. 32 - Andreas Wagner:
From bit to it: How a complex metabolic network transforms information into living matter. 33 - Grigoris D. Amoutzias, Elgar Pichler, Nina Mian, David De Graaf, Anastasia Imsiridou, Marc Robinson-Rechavi, Erich Bornberg-Bauer, David L. Robertson, Stephen G. Oliver:
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. 34 - Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi:
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. 35 - Fernando Siso-Nadal, Julien F. Ollivier, Peter S. Swain:
Facile: a command-line network compiler for systems biology. 36 - Rainer Opgen-Rhein, Korbinian Strimmer:
From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. 37 - Gustavo H. Esteves, Ana Carolina Quirino Simoes, Estevao Souza, Rodrigo A. Dias, Raydonal Ospina, Thiago M. Venancio:
New insights about host response to smallpox using microarray data. 38 - André Fujita, João Ricardo Sato, Humberto Miguel Garay-Malpartida, Rui Yamaguchi, Satoru Miyano, Mari Cleide Sogayar, Carlos Eduardo Ferreira:
Modeling gene expression regulatory networks with the sparse vector autoregressive model. 39 - Maria Werner, Ingemar Ernberg, JieZhi Zou, Jenny Almqvist, Erik Aurell:
Epstein-Barr virus latency switch in human B-cells: a physico-chemical model. 40 - Matt J. Hodgkinson, Penelope A. Webb:
A system for success: BMC Systems Biology, a new open access journal. 41 - Andreas Kremling, Katja Bettenbrock, Ernst Dieter Gilles:
Analysis of global control of Escherichia coli carbohydrate uptake. 42 - Takuya T. Maeda, Itsuki Ajioka, Kazunori Nakajima:
Computational cell model based on autonomous cell movement regulated by cell-cell signalling successfully recapitulates the "inside and outside" pattern of cell sorting. 43 - Mark Müller-Linow, Wolfram Weckwerth, Marc-Thorsten Hütt:
Consistency analysis of metabolic correlation networks. 44 - Claes R. Andersson, Torgeir R. Hvidsten, Anders Isaksson, Mats G. Gustafsson, Jan Komorowski:
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors. 45 - Scott H. Robertson, Chris K. Smith, Anna L. Langhans, Sara E. McLinden, Matthew A. Oberhardt, Karoly R. Jakab, Bette Dzamba, Douglas W. DeSimone, Jason A. Papin, Shayn M. Peirce:
Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior. 46 - Yiannis N. Kaznessis:
Models for synthetic biology. 47 - Harish Shankaran, H. Steven Wiley, Haluk Resat:
Receptor downregulation and desensitization enhance the information processing ability of signalling receptors. 48 - Kirill Evlampiev, Hervé Isambert:
Modeling protein network evolution under genome duplication and domain shuffling. 49 - Junwei Wang, Jiajun Zhang, Zhanjiang Yuan, Tianshou Zhou:
Noise-induced switches in network systems of the genetic toggle switch. 50 - Florian Steinke, Matthias W. Seeger, Koji Tsuda:
Experimental design for efficient identification of gene regulatory networks using sparse Bayesian models. 51 - Yu Feng Wu, Ekaterina M. Myasnikova, John Reinitz:
Master equation simulation analysis of immunostained Bicoid morphogen gradient. 52 - Miyako Kusano, Atsushi Fukushima, Masanori Arita, Pär Jonsson, Thomas Moritz, Makoto Kobayashi, Naomi Hayashi, Takayuki Tohge, Kazuki Saito:
Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. 53 - Peter Langfelder, Steve Horvath:
Eigengene networks for studying the relationships between co-expression modules. 54 - Heiko Neuweger, Jan Baumbach, Stefan P. Albaum, Thomas Bekel, Michael Dondrup, Andrea T. Hüser, Jörn Kalinowski, Sebastian Oehm, Alfred Pühler, Sven Rahmann, Jochen Weile, Alexander Goesmann:
CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. 55 - Danielle G. Lemay, Margaret C. Neville, Michael Rudolph, Katherine S. Pollard, J. Bruce German:
Gene regulatory networks in lactation: identification of global principles using bioinformatics. 56 - Arne B. Gjuvsland, Erik Plahte, Stig W. Omholt:
Threshold-dominated regulation hides genetic variation in gene expression networks. 57 - Camille Laibe, Nicolas Le Novère:
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology. 58
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